Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F1 I1 R1
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,615,722 |
+A |
intergenic (+48/‑141) |
prfA → / → h16_A3341 |
protein chain release factor A (RF‑1)/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,615,720 | 1 | . | A | 100.0%
| 125.4
/ NA
| 33 | intergenic (+46/‑143) | prfA/h16_A3341 | protein chain release factor A (RF‑1)/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base A (17/16); total (17/16) |
GCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCGA > AM260479/3615595‑3615841
|
gCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGT‑aaagtcg < 1:339408/134‑6 (MQ=255)
aTGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGa > 1:618364/1‑133 (MQ=255)
tCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCtt < 1:616266/134‑1 (MQ=255)
cTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGT‑aaagtcg > 2:957244/1‑103 (MQ=255)
cTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGT‑aaagtcg < 1:957244/108‑6 (MQ=255)
gATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAAc > 2:687736/1‑122 (MQ=255)
gATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAAc < 1:687736/122‑1 (MQ=255)
gATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAgg > 1:855057/1‑134 (MQ=255)
cAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAgggg > 1:945033/1‑133 (MQ=255)
gCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCAc < 2:1028461/122‑1 (MQ=255)
gCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCAc > 1:1028461/1‑122 (MQ=255)
aaGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCtt > 1:358207/1‑85 (MQ=255)
aaGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCtt < 2:358207/85‑1 (MQ=255)
aaGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATc > 2:890569/1‑134 (MQ=255)
caAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGcc < 1:465773/50‑1 (MQ=37)
caAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGcc > 2:465773/1‑50 (MQ=37)
aaaTGTCGTGCAACCGGCCTTCCGCCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAg < 2:948455/100‑1 (MQ=255)
aaaTGTCGTGCAACCGGCCTTCCGCCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAg > 1:948455/1‑100 (MQ=255)
aaaTGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACgg < 2:281804/134‑1 (MQ=255)
aaaTGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACg > 2:489132/1‑133 (MQ=255)
tGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGt > 2:12320/1‑134 (MQ=255)
cAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCAc < 1:467891/76‑1 (MQ=255)
cAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCAc > 2:467891/1‑76 (MQ=255)
aaCCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGcc > 1:758332/1‑134 (MQ=255)
aCCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCtt > 1:120069/1‑64 (MQ=255)
aCCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCtt < 2:120069/64‑1 (MQ=255)
aCCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCg > 1:659394/1‑134 (MQ=255)
gCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTa < 2:659394/134‑1 (MQ=255)
gCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTa < 1:12320/134‑1 (MQ=255)
ccTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTaaa > 2:525924/1‑54 (MQ=255)
ccTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTaaa < 1:525924/54‑1 (MQ=255)
cG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACgg > 2:375722/1‑112 (MQ=255)
cG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACgg < 1:375722/112‑1 (MQ=255)
cG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCAc < 2:346840/133‑1 (MQ=255)
cG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCAc < 2:855057/133‑1 (MQ=255)
cGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGTGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCga < 2:945033/134‑1 (MQ=255)
|
GCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCGA > AM260479/3615595‑3615841
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCGAGAACATACCTAGG > AM260479/3615585‑3615854
|
ATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGAT > GWNJ‑0478:712:GW2002102894th:2:2106:17947:65002/1‑149 (MQ=60)
GGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTAT < GWNJ‑0478:712:GW2002102894th:2:1207:16155:58704/150‑1 (MQ=60)
ataagagacagGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTAT < GWNJ‑0478:712:GW2002102894th:2:2212:9875:46544/138‑1 (MQ=60)
tttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTT < GWNJ‑0478:712:GW2002102894th:2:1212:1380:91969/80‑1 (MQ=60)
GTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAAC < GWNJ‑0478:712:GW2002102894th:2:2106:10548:51597/150‑1 (MQ=60)
caagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCAC < GWNJ‑0478:712:GW2002102894th:2:2101:13121:19833/84‑1 (MQ=60)
TCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGG > GWNJ‑0478:712:GW2002102894th:2:2209:3275:27187/1‑150 (MQ=60)
GGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGT < GWNJ‑0478:712:GW2002102894th:2:2110:17723:86580/150‑1 (MQ=60)
GAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGT > GWNJ‑0478:712:GW2002102894th:2:2210:5713:75230/1‑149 (MQ=60)
ACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTA > GWNJ‑0478:712:GW2002102894th:2:2216:3527:31567/1‑148 (MQ=60)
atgtagctccgtctcgtgggctcggagatgtgtataagagacagCCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGC < GWNJ‑0478:712:GW2002102894th:2:1215:9659:3758/106‑1 (MQ=60)
TTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACctgtctcttatacacatctccgagcccacgagacg > GWNJ‑0478:712:GW2002102894th:2:1206:17495:75542/1‑115 (MQ=60)
GTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCtgtctcttatacacatctc > GWNJ‑0478:712:GW2002102894th:2:2210:18176:95300/1‑131 (MQ=60)
CACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCG > GWNJ‑0478:712:GW2002102894th:2:2114:9178:85744/1‑150 (MQ=60)
ACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTActgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgt > GWNJ‑0478:712:GW2002102894th:2:1109:8578:6569/1‑94 (MQ=60)
ACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGG > GWNJ‑0478:712:GW2002102894th:2:2111:6490:22188/1‑150 (MQ=60)
agagacagGTGCAACCGGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGT < GWNJ‑0478:712:GW2002102894th:2:1208:13417:82398/142‑1 (MQ=60)
GGCCTTCCG‑CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCGAGAAC < GWNJ‑0478:712:GW2002102894th:2:1101:6918:90656/150‑1 (MQ=60)
CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGctgtctcttatacacatctccagcccacgagac > GWNJ‑0478:712:GW2002102894th:2:1208:6367:46912/1‑117 (MQ=60)
CCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCGAGAACATACCTAGG > GWNJ‑0478:712:GW2002102894th:2:2216:19555:40364/1‑150 (MQ=60)
|
ATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCG‑CCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCGAGAACATACCTAGG > AM260479/3615585‑3615854
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
